Bioinformatics Tools and Knowledgebases to Assist Generating Targeted Assays for Plasma Proteomics

Area of Science:

• Proteomics
• Bioinformatics
• Biotechnology

Background:

• Selecting proteotypic peptides is critical for targeted proteomics.
• This process typically involves complex bioinformatics analysis using various tools and databases.

Purpose of the Study:

• To present web-based resources that automate and simplify proteotypic peptide selection for targeted proteomics.
• To streamline targeted proteomics assay development, particularly for plasma proteins.

Main Methods:

• Introduction of bioinformatics tools: PeptidePicker, PeptidePickerDB, MRMAssayDB, MouseQuaPro, and PeptideTracker.
• Utilizing these tools for developing and documenting targeted proteomics assays.
• Integration of HUPO Human Plasma Proteome Project data to create a new assay database.

Main Results:

• Development of thousands of targeted proteomics assays, with a focus on human and mouse plasma proteins.
• Creation of a new database containing 3.8k targeted assays for known human plasma proteins.
• Demonstration of an integrative approach simplifying assay design and reducing experimental effort.

Conclusions:

• The presented web-based tools significantly streamline targeted proteomics assay development.
• These resources facilitate the quantitative characterization of the plasma proteome.
• Freely accessible tools enable efficient design of targeted proteomic experiments.